RGList_CALIB-class           package:CALIB           R Documentation

_R_e_d, _G_r_e_e_n _I_n_t_e_n_s_i_t_y _L_i_s_t - _C_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A simple list-based class for storing red and green channel
     foreground and  background intensities for a batch of spotted
     microarrays. It is a extension of  the RGList in the LIMMA
     package.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("RGList_CALIB",
     RG)', where RG is a list. In the CALIB package, RGList_CALIB
     objects are normally generated by 'read.rg'.

_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     objects should contain the following list components:

     '_R': numeric matrix containing the red(Cy5) foreground
          intensities. Rows correspond to spots and columns to arrays.

     '_G': numeric matrix containing the green(Cy3) foreground
          intensities.

     '_R_b': numeric matrix containing the red(Cy5) background
          intensities.

     '_G_b': numeric matrix containing the green(Cy3) background
          intensities.

     '_R_A_r_e_a': numeric matrix containing the red(Cy5) spot areas.

     '_G_A_r_e_a': numeric matrix containing the green(Cy3) spot areas.

     Optional components include:

     '_w_e_i_g_h_t_s': numeric matrix containing relative spot quality
          weights. Should be non-negative.

     '_p_r_i_n_t_e_r': list containing information on the process used to
          print the spots on the arrays. See 'read.rg'.

     '_g_e_n_e_s': data.frame containing information on the genes spotted on
          the arrays. Should include a character column Name containing
          names for the genes or controls.

     '_t_a_r_g_e_t_s': data.frame containing information on the target RNA
          samples. Should include factor or character columns Cy3 and
          Cy5 specifying which RNA was hybridized to each array.

     '_o_t_h_e_r': list containing numeric matrices of other spot-specific
          information.

     All of the matrices should have the same dimensions. The row
     dimension of targets should match the column dimension of the
     matrices.

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"LargeDataObject"',
     directly. Class '"vector"', by class '"list"'.

_M_e_t_h_o_d_s:

     This class inherits directly from class List so any operation
     appropriate for lists will work on objects of this class. In
     addition, RGList_CALIB objects can be 'subsetted', 'combined' and
     'merged'. RGList_CALIB objects will return dimensions and hence
     functions such as 'dim', 'dimnames', 'nrow' and 'ncol' are
     defined. RGList_CALIB also inherit a 'show' method from the
     virtual class 'LagerDataObject', which means that RGList_CALIB
     objects will print in a compact way.

     In the CALIB package, RGList_CALIB objects are mainly for storing
     microarray data and they are used to pass microarray data into
     functions such as 'estimateParameter' or 'normalizeData'.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     'RGList' in the limma package

_S_e_e _A_l_s_o:

     'RGList' and 'LargeDataObject' in limma packge.

